Files "disappeared" in Vista

I was called by a friend who is still using Vista. It seems that, as a result of malware, all of her folders appear to be empty. Explorer shows the directory trees with the folders, but clicking on a folder does nothing. I inserted a usb stick which has various utilities, etc. to run some diagnostics. I could not see the contents of any folders on the usb stick or any of the files at all! I then downloaded tdsskiller and installed it but, of course, the .exe file was not visible in Explorer or in ExplorerPlus. Fortunately, I can copy folders to an external usb stick and they open just fine on another computer so the data is backed up. I downloaded Malwarebytes which, after installation, runs the file. A quick scan showed no malware.I am pretty convinced that there is a rootkit problem but I don't know of an effective rootkit cleanup program which automatically opens after the installation is complete.